Four months after the events of Peter's explosion, we find the heroes at different places in their lives. Claire, HRG and family try to stay below the radar in their new town, but a classmate of Claire's with some powers of his own knows there's something different about her. Matt Parkman and Mohinder Suresh are now guardians of Molly Parker, who has been suffering from horrible nightmares about the man who is more evil than Sylar. Mohinder and HRG are still trying to take the company down. Kaito Nakamura and Angela Petrelli receive ominous notices of their impending deaths, clearly sent by one of "the elders". Nathan has pushed his family away and is in a very dark place, feeling that Peter has survived and is alive somewhere. In Ireland, we find Peter Petrelli is alive, but doesn't remember who he is. Maya and Alejandro, two new characters, are wanted for murder due to her accidentally killing multiple people because of her ability to host a plague.

At the behest of his new employers, Dr. Suresh travels to Haiti to treat a potential virus victim. The patient turns out to be a familiar face. Claire's secret may be out when a fellow student sees her regenerate a limb; that student may have his own secret however. Matt Parkman investigates a murder that affects one one of the Heroes. In 17th century Japan, Hiro is doing his best to ensure that Takezo Sensei lives up to his reputation. He has to take things into his own hands however. In Ireland, Peter Petrelli finds himself with no memory but re-discovering some of his many powers. Maya and her brother reach the Guatemala-Mexico border in their quest to travel to the USA.

Micah warms his way into his cousin's heart by using his powers. Matt gets closer to finding some answers surrounding the mysterious mark on Hiro's father's photo and asks Molly to help him. Nathan's mother confesses to killing Hiro's father, and Claire grows closer to the classmate who can fly.

Hiro learns of his father's death and travels back in time to save him only to realize that he must let events unfold as fate intended. He does however recognize his father's killer. Matt Parkman realizes that he has the ability to implant thoughts in other people's minds. He wants to know the identity of the woman in the photo with his father. When Bob and Suresh kidnap Claire Bennet, HRG and West set out to rescue her but get their own bargaining chip beforehand.